there was vibration when i would go into 4th gear and 5th gear.
Was the vibration present with both transmissions that cracked? That may well be your smoking gun. A vibration in 4th and 5th gear suggests it is coming on with vehicle speed which would likely be an issue in the driveshaft. You should definitely look over the driveshaft to make sure the u-joints are centered and in good shape, clips are in place, you have the proper size u-joint for the rear axle, and get the balance checked. I have seen new driveshafts that were not balanced properly. If you bring it back to the same shop that built it and they say it is good, I would consider checking with another shop. Before having it balanced, make sure you have enough free travel in the yoke so that it is not bottoming out with suspension travel. While checking all this, you better check your rear axle yoke to make sure it is not loose.
You can usually narrow down a vibration as being engine/trans related vs driveshaft related by slowly revving engine up to normal cruise rpm while sitting still. If you pick up the vibration doing this, it is engine or trans. If not, it is usually driveshaft, u-joints, etc.